6-10982740-T-C

Position:

• chr6-10982740-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017770.4(ELOVL2):​c.*1041A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 152,032 control chromosomes in the GnomAD database, including 15,391 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.43 (15390 hom., cov: 32)
  • Exomes 𝑓: 0.50 (1 hom.)
• Consequence: ELOVL2 NM_017770.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.339

Genes affected

ELOVL2 (HGNC:14416): (ELOVL fatty acid elongase 2) Enables fatty acid elongase activity. Involved in fatty acid elongation, polyunsaturated fatty acid and very long-chain fatty acid biosynthetic process. Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.884 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELOVL2	NM_017770.4	c.*1041A>G		3_prime_UTR_variant	8/8	ENST00000354666.4
ELOVL2	XM_011514716.4	c.*1041A>G		3_prime_UTR_variant	8/8
ELOVL2	XM_011514717.4	c.*1041A>G		3_prime_UTR_variant	8/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELOVL2	ENST00000354666.4	c.*1041A>G		3_prime_UTR_variant	8/8	1	NM_017770.4	P1

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64577 AN: 151906 Hom.: 15372 Cov.: 32

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.906

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.447

GnomAD4 exome AF: 0.500 AC: 4 AN: 8 Hom.: 1 Cov.: 0 AF XY: 0.250 AC XY: 1 AN XY: 4

Gnomad4 AFR exome AF: 0.500

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.425 AC: 64624 AN: 152024 Hom.: 15390 Cov.: 32 AF XY: 0.436 AC XY: 32383 AN XY: 74290

Gnomad4 AFR AF: 0.251

Gnomad4 AMR AF: 0.582

Gnomad4 ASJ AF: 0.553

Gnomad4 EAS AF: 0.906

Gnomad4 SAS AF: 0.656

Gnomad4 FIN AF: 0.472

Gnomad4 NFE AF: 0.430

Gnomad4 OTH AF: 0.452

Alfa AF: 0.441 Hom.: 33959

Bravo AF: 0.425

Asia WGS AF: 0.731 AC: 2539 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.9
DANN	Benign	0.57

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3734398; hg19: chr6-10982973;